[2024-01-24 13:22:14,639] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:14,641] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:14,642] [INFO] DQC Reference Directory: /var/lib/cwl/stg11244f5b-0f76-4cf3-b68d-f60e1af14461/dqc_reference
[2024-01-24 13:22:15,920] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:15,920] [INFO] Task started: Prodigal
[2024-01-24 13:22:15,921] [INFO] Running command: gunzip -c /var/lib/cwl/stg4900ca26-d17b-465b-87bc-6449c2e4d749/GCF_900106975.1_IMG-taxon_2671180037_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900106975.1_IMG-taxon_2671180037_annotated_assembly_genomic.fna/cds.fna -a GCF_900106975.1_IMG-taxon_2671180037_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:30,135] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:30,136] [INFO] Task started: HMMsearch
[2024-01-24 13:22:30,136] [INFO] Running command: hmmsearch --tblout GCF_900106975.1_IMG-taxon_2671180037_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg11244f5b-0f76-4cf3-b68d-f60e1af14461/dqc_reference/reference_markers.hmm GCF_900106975.1_IMG-taxon_2671180037_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:30,578] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:30,579] [INFO] Found 6/6 markers.
[2024-01-24 13:22:30,621] [INFO] Query marker FASTA was written to GCF_900106975.1_IMG-taxon_2671180037_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:22:30,622] [INFO] Task started: Blastn
[2024-01-24 13:22:30,622] [INFO] Running command: blastn -query GCF_900106975.1_IMG-taxon_2671180037_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg11244f5b-0f76-4cf3-b68d-f60e1af14461/dqc_reference/reference_markers.fasta -out GCF_900106975.1_IMG-taxon_2671180037_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:31,699] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:31,702] [INFO] Selected 22 target genomes.
[2024-01-24 13:22:31,702] [INFO] Target genome list was writen to GCF_900106975.1_IMG-taxon_2671180037_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:22:31,710] [INFO] Task started: fastANI
[2024-01-24 13:22:31,710] [INFO] Running command: fastANI --query /var/lib/cwl/stg4900ca26-d17b-465b-87bc-6449c2e4d749/GCF_900106975.1_IMG-taxon_2671180037_annotated_assembly_genomic.fna.gz --refList GCF_900106975.1_IMG-taxon_2671180037_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900106975.1_IMG-taxon_2671180037_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:55,572] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:55,572] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg11244f5b-0f76-4cf3-b68d-f60e1af14461/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:55,573] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg11244f5b-0f76-4cf3-b68d-f60e1af14461/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:55,589] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:55,590] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:55,590] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Pseudomonas kuykendallii	strain=NRRL B-59562	GCA_900106975.1	1007099	1007099	type	True	100.0	1556	1557	95	conclusive
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	82.7568	885	1557	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	82.6481	866	1557	95	below_threshold
Pseudomonas delhiensis	strain=CCM 7361	GCA_900099945.1	366289	366289	type	True	82.6399	975	1557	95	below_threshold
Pseudomonas delhiensis	strain=RLD-1	GCA_900187975.1	366289	366289	type	True	82.6274	976	1557	95	below_threshold
Pseudomonas jinjuensis	strain=NBRC 103047	GCA_002091655.1	198616	198616	type	True	82.5349	890	1557	95	below_threshold
Pseudomonas jinjuensis	strain=JCM 21621	GCA_900103845.1	198616	198616	type	True	82.4688	899	1557	95	below_threshold
Pseudomonas campi	strain=S1-A32-2	GCA_013200955.2	2731681	2731681	type	True	82.3384	824	1557	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	82.2808	866	1557	95	below_threshold
Pseudomonas guryensis	strain=SR9	GCA_014164785.1	2759165	2759165	type	True	82.1589	803	1557	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	82.1144	704	1557	95	below_threshold
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	82.0571	725	1557	95	below_threshold
Pseudomonas linyingensis	strain=LMG 25967	GCA_900109175.1	915471	915471	type	True	81.9065	728	1557	95	below_threshold
[Pseudomonas] nosocomialis	strain=A31/70	GCA_005876855.1	1056496	1056496	type	True	81.6655	797	1557	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	81.5075	766	1557	95	below_threshold
Pseudomonas flexibilis	strain=ATCC 29606	GCA_000802425.1	706570	706570	type	True	81.5054	682	1557	95	below_threshold
Pseudomonas flexibilis	strain=ATCC 29606	GCA_900155995.1	706570	706570	type	True	81.4991	674	1557	95	below_threshold
Stutzerimonas stutzeri	strain=CGMCC 1.1803	GCA_000219605.1	316	316	type	True	81.2722	771	1557	95	below_threshold
Stutzerimonas stutzeri	strain=FDAARGOS_875	GCA_016028655.1	316	316	type	True	81.1987	790	1557	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	81.0923	784	1557	95	below_threshold
Pseudomonas psychrotolerans	strain=DSM 15758	GCA_900102665.1	237610	237610	suspected-type	True	80.2767	731	1557	95	below_threshold
Pseudomonas rhizoryzae	strain=RY24	GCA_005250615.1	2571129	2571129	type	True	80.0444	690	1557	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:55,596] [INFO] DFAST Taxonomy check result was written to GCF_900106975.1_IMG-taxon_2671180037_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:22:55,596] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:55,597] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:55,597] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg11244f5b-0f76-4cf3-b68d-f60e1af14461/dqc_reference/checkm_data
[2024-01-24 13:22:55,598] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:55,649] [INFO] Task started: CheckM
[2024-01-24 13:22:55,649] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900106975.1_IMG-taxon_2671180037_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900106975.1_IMG-taxon_2671180037_annotated_assembly_genomic.fna/checkm_input GCF_900106975.1_IMG-taxon_2671180037_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:23:38,818] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:38,820] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:38,843] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:38,844] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:38,844] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900106975.1_IMG-taxon_2671180037_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:23:38,844] [INFO] Task started: Blastn
[2024-01-24 13:23:38,845] [INFO] Running command: blastn -query GCF_900106975.1_IMG-taxon_2671180037_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg11244f5b-0f76-4cf3-b68d-f60e1af14461/dqc_reference/reference_markers_gtdb.fasta -out GCF_900106975.1_IMG-taxon_2671180037_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:41,179] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:41,188] [INFO] Selected 20 target genomes.
[2024-01-24 13:23:41,188] [INFO] Target genome list was writen to GCF_900106975.1_IMG-taxon_2671180037_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:41,214] [INFO] Task started: fastANI
[2024-01-24 13:23:41,214] [INFO] Running command: fastANI --query /var/lib/cwl/stg4900ca26-d17b-465b-87bc-6449c2e4d749/GCF_900106975.1_IMG-taxon_2671180037_annotated_assembly_genomic.fna.gz --refList GCF_900106975.1_IMG-taxon_2671180037_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900106975.1_IMG-taxon_2671180037_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:04,363] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:04,379] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:04,380] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_900106975.1	s__Pseudomonas_O kuykendallii	100.0	1556	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_O	95.0	96.83	96.68	0.93	0.91	4	conclusive
GCA_002418465.1	s__Pseudomonas_O sp002418465	91.2749	1065	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_O	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506505.1	s__Pseudomonas_E sp902506505	83.1623	856	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.45	95.45	0.88	0.88	2	-
GCF_009799925.1	s__Pseudomonas_E sp009799925	83.1579	858	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904061905.1	s__Pseudomonas_E carbonaria	83.0185	916	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003205495.1	s__Pseudomonas_E alcaligenes_B	82.9425	857	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014851905.1	s__Pseudomonas_E sp014851905	82.8517	944	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016901015.1	s__Pseudomonas_E sp016901015	82.7708	885	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187975.1	s__Pseudomonas delhiensis	82.6618	970	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.078	98.79	97.59	0.94	0.89	3	-
GCF_900103845.1	s__Pseudomonas jinjuensis	82.472	899	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014174475.1	s__Pseudomonas_E sp014174475	82.4116	856	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007109405.1	s__VJOY01 sp007109405	82.2656	868	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__VJOY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014164785.1	s__Pseudomonas_E sp014164785	82.1972	799	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005876855.1	s__Pseudomonas_R nosocomialis	81.6984	793	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_R	95.0	98.98	98.95	0.91	0.90	3	-
GCF_000802425.1	s__Pseudomonas_H flexibilis	81.4983	683	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_H	95.0	99.07	98.74	0.94	0.90	5	-
GCF_000219605.1	s__Pseudomonas_A stutzeri	81.2736	770	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.69	96.98	0.90	0.83	156	-
GCF_003205815.1	s__Pseudomonas_A sp003205815	81.1307	782	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.18	96.58	0.91	0.87	27	-
GCF_001512295.1	s__Pseudomonas_B sp001512295	80.2746	714	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014522265.1	s__Pseudomonas_B oryzihabitans_D	80.2636	694	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	96.63	95.05	0.89	0.84	6	-
GCF_001650425.1	s__Pseudomonas_B oryzihabitans_B	80.0585	683	1557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	97.78	97.39	0.90	0.88	6	-
--------------------------------------------------------------------------------
[2024-01-24 13:24:04,382] [INFO] GTDB search result was written to GCF_900106975.1_IMG-taxon_2671180037_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:04,382] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:04,387] [INFO] DFAST_QC result json was written to GCF_900106975.1_IMG-taxon_2671180037_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:24:04,387] [INFO] DFAST_QC completed!
[2024-01-24 13:24:04,387] [INFO] Total running time: 0h1m50s